Hi

The aluminum can be laser cut and engraved by services such as Ponoko
The black lid will print fine on an FDM printer. I would remodel it rather than 3D scan it but if it's a good scanner it will work either way.
For the transparent inset I would also use a laser cutting service since it will never become clear like that with 3D printing. Plexiglass, PC or acrylic will work.